isse #121 test #20

src/test/java/edu/ucsd/sbrg/bigg/annotation/ReactionAnnotationTest.java

@@ -0,0 +1,79 @@
+package edu.ucsd.sbrg.bigg.annotation;
+
+import org.junit.jupiter.api.Test;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.fbc.FBCConstants;
+import org.sbml.jsbml.ext.fbc.FBCReactionPlugin;
+import org.sbml.jsbml.ext.fbc.GeneProductRef;
+import org.sbml.jsbml.ext.groups.GroupsConstants;
+import org.sbml.jsbml.ext.groups.GroupsModelPlugin;
+import org.sbml.jsbml.ext.groups.Member;
+
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static edu.ucsd.sbrg.TestUtils.initParameters;
+import static org.junit.jupiter.api.Assertions.*;
+
+public class ReactionAnnotationTest extends BiGGDBTest {
+
+    @Test
+    public void getBiGGIdFromResourcesTest() {
+        initParameters();
+        var m = new Model("iJO1366", 3, 2);
+        var r1 = m.createReaction("some_name");
+        var r2 = m.createReaction("some_other_name");
+        var r3 = m.createReaction("some_third_name");
+
+        r1.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "http://identifiers.org/biocyc/META:ACETATEKIN-RXN"));
+
+        r2.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "http://identifiers.org/metanetx.reaction/MNXR103371"));
+
+        r3.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "http://identifiers.org/kegg.reaction/R00299"));
+
+        var gPlugin = (GroupsModelPlugin) m.getPlugin(GroupsConstants.shortLabel);
+        assertEquals(0, gPlugin.getGroupCount());
+
+        new ReactionAnnotation(r1).annotate();
+        new ReactionAnnotation(r2).annotate();
+        new ReactionAnnotation(r3).annotate();
+
+        var r1FbcPlugin = (FBCReactionPlugin) r1.getPlugin(FBCConstants.shortLabel);
+        var gpa1 =  r1FbcPlugin.getGeneProductAssociation();
+        assertNull(gpa1);
+        assertEquals(false, r1.isSetCompartment());
+        assertEquals("", r1.getName());
+        assertEquals(1, r1.getCVTermCount());
+        assertEquals(1, r1.getCVTerm(0).getNumResources());
+
+        assertEquals(1, r2.getCVTermCount());
+        assertEquals(1, r2.getCVTerm(0).getNumResources());
+
+        var r3FbcPlugin = (FBCReactionPlugin) r3.getPlugin(FBCConstants.shortLabel);
+        var gpa3 =  r3FbcPlugin.getGeneProductAssociation();
+        assertNotNull(gpa3);
+        assertEquals("G_b2388", ((GeneProductRef) gpa3.getAssociation()).getGeneProduct());
+        assertEquals(false, r1.isSetCompartment());
+        assertEquals("", r1.getName());
+        assertEquals(1, r3.getCVTermCount());
+        assertEquals(11, r3.getCVTerm(0).getNumResources());
+
+        assertEquals(1, gPlugin.getGroupCount());
+        assertEquals("glycolysis/gluconeogenesis", gPlugin.getGroup(0).getName());
+        assertEquals(Set.of("some_third_name"), gPlugin.getGroup(0)
+                .getListOfMembers().stream().map(Member::getIdRef).collect(Collectors.toSet()));
+
+        assertFalse(r3.isSetListOfReactants());
+        assertFalse(r3.isSetListOfProducts());
+    }
+}

src/test/java/edu/ucsd/sbrg/bigg/annotation/SpeciesAnnotationTest.java

@@ -1,17 +1,19 @@
 package edu.ucsd.sbrg.bigg.annotation;
 
 import edu.ucsd.sbrg.TestUtils;
+import edu.ucsd.sbrg.bigg.ModelPolisherOptions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.sbml.jsbml.CVTerm;
 import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.ext.fbc.FBCConstants;
 import org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin;
 
+import java.util.Map;
 import java.util.Set;
 
-import static edu.ucsd.sbrg.TestUtils.assertCVTermIsPresent;
-import static edu.ucsd.sbrg.TestUtils.assertCVTermsArePresent;
+import static edu.ucsd.sbrg.TestUtils.*;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class SpeciesAnnotationTest extends BiGGDBTest {
@@ -195,5 +197,39 @@ public void H2OAnnotationTest() {
 
     }
 
+    /**
+     * Same principle as above, just testing for kegg and biocyc too.
+     */
+    @Test
+    public void getBiGGIdFromResourcesTest() {
+        initParameters(Map.of(
+                ModelPolisherOptions.ANNOTATE_WITH_BIGG.getOptionName(),
+                "true",
+                ModelPolisherOptions.INCLUDE_ANY_URI.getOptionName(),
+                "true"));
+        var sbml = new SBMLDocument(3, 2);
+        var m = new Model("iJO1366", 3, 2);
+        sbml.setModel(m);
+        var s1 = m.createSpecies("some_name");
+        var s2 = m.createSpecies("some_other_name");
+
+        s1.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/kegg.compound/C00001"));
+
+        s2.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/biocyc/META:ATP"));
+
+        var annotater = new BiGGAnnotation();
+        annotater.annotate(sbml);
+
+        assertEquals(1, s2.getCVTermCount());
+        assertEquals(29, s1.getCVTerm(0).getNumResources());
+        assertEquals(1, s2.getCVTermCount());
+        assertEquals(30, s2.getCVTerm(0).getNumResources());
+    }
 
 }